6UQB

Crystal structure of R471A variant of cytosolic fumarate hydratase from Leishmania major in a complex with S-malate and malonate

  • Classification: LYASE
  • Organism(s): Leishmania major
  • Expression System: Escherichia coli
  • Mutation(s): 

  • Deposited: 2019-10-18 Released: 2019-12-04 
  • Deposition Author(s): Feliciano, P.R., Drennan, C.L.
  • Funding Organization(s): Sao Paulo Research Foundation (FAPESP); Howard Hughes Medical Institute (HHMI); National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.951 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Biochemical Investigations of the [4Fe-4S] Cluster-Containing Fumarate Hydratase fromLeishmania major.

Feliciano, P.R.Drennan, C.L.

(2019) Biochemistry 58: 5011-5021

  • DOI: 10.1021/acs.biochem.9b00923
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Class I fumarate hydratases (FHs) are central metabolic enzymes that use a [4Fe-4S] cluster to catalyze the reversible conversion of fumarate to <i>S </i>-malate. The parasite <i>Leishmania major </i>, which is responsible for leishmaniasis, expres ...

    Class I fumarate hydratases (FHs) are central metabolic enzymes that use a [4Fe-4S] cluster to catalyze the reversible conversion of fumarate to S -malate. The parasite Leishmania major , which is responsible for leishmaniasis, expresses two class I FH isoforms: mitochondrial LmFH-1 and cytosolic LmFH-2. In this study, we present kinetic characterizations of both LmFH isoforms, present 13 crystal structures of LmFH-2 variants, and employ site-directed mutagenesis to investigate the enzyme's mechanism. Our kinetic data confirm that both LmFH-1 and LmFH-2 are susceptible to oxygen-dependent inhibition, with data from crystallography and electron paramagnetic resonance spectroscopy showing that oxygen exposure converts an active [4Fe-4S] cluster to an inactive [3Fe-4S] cluster. Our anaerobically conducted kinetic studies reveal a preference for fumarate over S -malate. Our data further reveal that single alanine substitutions of T467, R421, R471, D135, and H334 decrease k cat values 9-16000-fold without substantially affecting K m values, suggesting that these residues function in catalytic roles. Crystal structures of LmFH-2 variants are consistent with this idea, showing similar bidentate binding to the unique iron of the [4Fe-4S] cluster for substrate S -malate as observed in wild type FH. We further present LmFH-2 structures with substrate fumarate and weak inhibitors succinate and malonate bound in the active site and the first structure of an LmFH that is substrate-free and inhibitor-free, the latter showing increased mobility in the C-terminal domain. Collectively, these data provide insight into the molecular basis for the reaction catalyzed by LmFHs, enzymes that are potential drug targets against leishmaniasis.


    Organizational Affiliation

    Howard Hughes Medical Institute , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States.,Department of Biology , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States.,Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fumarate hydratase 2
A, B
604Leishmania majorMutation(s): 1 
Gene Names: FH2
EC: 4.2.1.2
Find proteins for E9AE57 (Leishmania major)
Go to UniProtKB:  E9AE57
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
LMR
Query on LMR

Download SDF File 
Download CCD File 
A, B
(2S)-2-hydroxybutanedioic acid
L-Malate
C4 H6 O5
BJEPYKJPYRNKOW-REOHCLBHSA-N
 Ligand Interaction
MLA
Query on MLA

Download SDF File 
Download CCD File 
A, B
MALONIC ACID
DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; METHANEDICARBOXYLIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.951 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.143 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.462α = 90.00
b = 84.943β = 90.00
c = 240.266γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2014/22246-4
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM126982

Revision History 

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2019-12-18
    Type: Database references